1. Archives and Information Retrieval
CSC 487/687 Computing for Bioinformatics

2. Introduction Learning objectives:
What is the general arrangement of biological data in the public databases?
To know the information retrieval skills that will allow you to make effective use of the databases.
To become familiar with basic operations.
How does one retrieve information on a particular subject in the literature?
Tutorial embedded in many databanks, which make it easy to explore their facilities.

3. Primary public domain bioinformatics servers
Facilities
European Bioinformatics
Institute (EBI)
United Kingdom
National Center
For Biotechnology
Information (NCBI)
United States
Genome
Net
(KEGG & DDBJ)
Japan
Databases
Analysis
Tools
Data library, National Institute of genetics, Janpan, DNA Data Bank

4. The Archives Massive biological experimental data
These biological information databases can be classified into two types
The first level databases
Come from the raw data which were obtained via the experiments. “simple”
The second level databases
Further reorganized based on.. in order to achieve some specific goals
the original data which obtains to the experiment, only passes through the simple classification reorganization and the annotation;

5. The Archives Some examples: The first level databases
Nucleic acid sequence databases: GenBank, EMBL Data Library, DNA Database of Japan (DDBJ)
Protein sequence database: SWISS-PROT, PIR
Protein structure database: PDB
The second level databases
GDB
TRANSFAC
SCOP
GDB Human Genome Database: a center for the collection of human genetic mapping data, its use of world-class leaders in human genetics to act as curators for the data.
TRANSFAC is the database on eukaryotic transcription factors, their genomic binding sites and DNA-binding profiles. SCOP: Structural Classification of Proteins

6. Nucleic acid sequence databases
International DNA Sequence Database Collaboration
NCBI (GenBank) – USA (1982)
EMBL (Data Library)– Europe (1982)
DDBJ (DNA Data Bank)– Japan (1988)
Triple partnership, National Center for biotechnology Information (USA), European Bioinformatics Institute , National Institute of Genetics. The raw data are identical, but the format in which they are stored, and the nature of the annotation vary among them

7. NCBI
Established in USA in 1988 as a national resource for molecular biology information
creates public databases
conducts research in computational biology
develops software tools for analyzing genome data
disseminates biomedical information
- all for the better understanding of molecular processes affecting human health and disease.

8. Nucleic acid sequence databases
GenBank
nucleic acid sequence and the protein sequence
literature work
biological annotation
A new release is made every two months
GenBank information retrieval system
The Genbank storehouse has contained all known nucleic acid sequence and the protein sequence, as well as literature work and biology annotation which is connected with them.
GenBank is an annotated collection of all DNA sequences. A new release of GenBank is made every two months. GenBank is part of the International Nucleotide Sequence Database Collaboration which also includes the DNA DataBank of Japan (DDBJ) and the European Molecular Biology Laboratory (EMBL). The data are exchanged among these three organization on a daily basis. GenBank is the primary sequence repository. It contains the annotated sequences submitted by the original authors and only the original authors can change them.

9. NCBI ENTREZ
A platform that provides access to and links to databases with biological information
ENTREZ
PubMed
GenBank
Protein
databases
Genomes
PopSet
Taxonomy
OMIM
MedLine
Entrez offers access through the following database divisions

10. NCBI ENTREZ Literature Database
GenBank
Protein
databases
Genomes
PopSet
Taxonomy
OMIM
MedLine
Literature Database
Database of DNA sequences that have been collected to
analyze the evolutionary relatedness of a population.
Database of human genes and genetic disorders
Database of all publicly available DNA sequences
Database of amino acid sequences from SwissProt, PIR, PRF,
PDB, and translations from annotated coding regions in
GenBank and RefSeq.
Database of genomes from organisms and viruses
Database of names of organisms with sequences in GenBank or Prot
PubMed Central
PubMed Central (PMC) is the U.S. National Library of Medicine's digital archive of life sciences journal literature. Access to the full text of articles in PMC is free, except where a journal requires a subscription for access to recent articles
OMIM Database
The OMIM (Online Mendelian Inheritance in Man) database is a catalog of human genes and genetic disorders. See OMIM and OMIM Help.
The Reference Sequence (RefSeq) collection aims to provide a comprehensive, integrated, non-redundant set of sequences, including genomic DNA, transcript (RNA), and protein products, for major research organisms.
RefSeq standards serve as the basis for medical, functional, and diversity studies; they provide a stable reference for gene identification and characterization, mutation analysis, expression studies, polymorphism discovery, and comparative analyses. RefSeqs are used as a reagent for the functional annotation of some genome sequencing projects, including those of human and mouse.
Taxonomy Database
The Taxonomy database contains the names of all organisms that are represented in the NCBI genetic database by at least one nucleotide or protein sequence
PopSet Database
The PopSet database contains aligned sequences submitted as a set resulting from a population, phylogenetic, or mutation study. These alignments describe such events as evolution and population variation.

11. PubMed Center
the U.S. National Library of Medicine's digital archive of life sciences journal literature
Access to the full text of articles in PMC is free, except where a journal requires a subscription for access to recent articles

12. OMIM-Online Mendelian Inheritance in Man
A catalog of human genes linked to diseases
Began by Victor A. McKusick at Johns Hopkins University
A good place to start when you want to research a certain disease or biological molecule
This database is cross-referenced to PubMed and other NCBI-based databases
OMIM Database
The OMIM (Online Mendelian Inheritance in Man) database is a catalog of human genes and genetic disorders. See OMIM and OMIM Help.

13. How to submit sequence data to GenBank
Bankit based web interface
Sequin program

14. On-class exercise

15. Protein databases
The Protein Information Resource (PIR) was established in 1984 by the National Biomedical Research Foundation (NBRF).
The PIR Protein Sequence Database evolved from the original NBRF Protein Sequence Database, developed over 20 years
PIR-International is a collaboration between NBRF, the Munich Information Center for Protein Sequences (MIPS), and the Japan International Protein Information Database (JIPID)
collect and publish what is now the oldest and largest database of biomolecular sequence, source, literature, and feature information.

16. PIR
PIR-International Protein Sequence Database: an annotated, non-redundant and cross-referenced database of protein sequences.
PIR Alignment Database, PIR-ALN: contains sequence alignments of superfamilies, families and homology domains produced from information in the Protein Sequence Database.
FAMBASE Family Database: a searchable database containing a single representative sequence from each protein family.
RESID Database of Amino Acid Modifications: based on feature information in the Protein Sequence Database.
major nucleic acid, literature, genome, structure, sequence alignment and family databases
PIR maintains several auxiliary databases to help annotation and for integrity checking. These include: PIR-ALN, containing alignments of superfamilies, families and homology domains; FAMBASE, a searchable database of family representatives; and the RESID Database of covalent protein modifications. All the Databases can be accessed on the PIR Web site ( and contain hypertext-links to each other and relevant external databases. The Web site is being redesigned to include new BLAST similarity search engines and pattern matching capabilities. The latest quarterly release of the databases can be accessed through the ATLAS multi-database retrieval software on the Atlas CD-ROM and downloaded by FTP

17. PIR

18. SWISS-PROT http://www.ebi.ac.uk/swissprot/
an well-annotated protein sequence database established in 1986.
It is maintained collaboratively by the Swiss Institute for Bioinformatics (SIB) and the European Bioinformatics Institute (EBI).
a curated protein sequence database that provides a high level of annotation, a minimal level of redundancy and a high level of integration with other databases. Note: UniProtKB/TrEMBL and UniProtKB/Swiss-Prot have been incorporated into the UniProt (Universal Protein Resource). a one-stop shop allowing easy access to all publicly available information about protein sequences.

19. PROSITE http://ca.expasy.org/prosite/
a method of determining what is the function of uncharacterized proteins translated from genomic or cDNA sequences.
a database of biologically significant sites
patterns formulated in such a way that with appropriate computational tools it can rapidly and reliably identify to which known family of protein (if any) the new sequence belongs.

20. PDB http://www.rcsb.org/pdb/
The single international repository for public data on the 3-dimensional structures of biological macromolecules
Is established by the Brookhaven National Lab of United States
The contents are primarily experimental data derived from X-ray crystallography and NMR experiments
Rasmol may demonstrate 3D structure of the biological macromolecule according to the PDB document
The Protein Data Bank (PDB) is the single international repository for public data on the 3-dimensional structures of biological macromolecules